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Commit 83a04a68 authored by Arin Wongprommoon's avatar Arin Wongprommoon
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tweak!(core): Change default window size of detrend

WHY IS THIS CHANGE NEEDED?:
- Sliding window detrending imposes oscillations onto time series.
  The period of these oscillations is determined by the size of the
  window.
- I discovered this by varying the window size on my analysis of real data.

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- Re-defined the window size to match the period of a cell division
  cycle/yeast metabolic cycle under favourable conditions, assuming
  image sampling every 5 minutes (most common setting).  Detrend process
  is used mainly in pre-processing to study biological oscillations --
  the process removes long-term trends that may obscure these
  oscillations.
- Changing the default parameter value does not solve the problem per
  se, but if the window size corresponds to the oscillation frequency,
  it will only reinforce these oscillations.

WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- Will change behaviour of skeletons scripts that rely on detrend,
  especially when no parameter value is defined.  Users have to be aware
  of the new default value and may have to adjust the parameter value to
  suit their data.

REFERENCES:
- Issue #22
parent f192bb9e
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......@@ -16,7 +16,7 @@ class detrendParameters(ParametersABC):
Size of sliding window.
"""
_defaults = {"window": 45}
_defaults = {"window": 16}
class detrend(PostProcessABC):
......
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